Runaway Intersect
by EdgarCaskett22
Summary: What would happen if Casey's kill order on Chuck didn't get canceled? Would he have gone through with it? What would have happened to Chuck and Sarah? What would become of the Intersect. That is where this story begins. Rated T
1. Chapter 1

Disclaimer- I do not own the show Chuck or have rights to any of its characters or locals.

**The Runaway Intersect**

Chapter 1

The date was July 26th, 2008. The place was Burbank California, a small apartment complex inside Echo Park. The person was Major John Casey with the NSA. John Casey had a normal job too, he worked at a retail outlet called BUYMORE, as a sales clerk. This job was his cover, to monitor and protect an asset named Charles Bartowski.

Casey was situated in his temporary home, inside his apartment. He opened an arm of his lazy-boy recliner, to reveal a small cash of buttons one wouldn't normally see on such a chair. Casey pushed a six number sequence of the buttons. A secret screen arose from the floorboards in his living room. A small woman, seated in a large leather chair, appeared on the screen. She was accompanied by a tall, menacing looking, man in a high dollar suit.

The small yet commanding woman began to speak. "It's time Major. Operation Bartowski is to come to an end. The final preparations for the new intersect is underway. All the tests have been good and the final product should be ready by tonight. Major, do we understand each other? I am giving you a direct order. Kill Chuck Bartowski, the minute you hear from me about the new intersect." Casey's face was blank during the entire briefing. The secret screen in John Casey's apartment went black again, quickly disappearing back into the floorboards.

Major John Casey had gotten orders before, and he would get new orders after this was all said and done. However, this was the first time he had ever questioned what he was tasked, even in the back of his own mind. For Casey, the government's orders were absolute. They were law.

Chuck Bartowski had never been so bored in his life, twelve long hours of video monitoring, that he was asked to look through by General Beckman and Agent Graham. This left Chuck with a sore brain and weary eyes. He was supposed to flash, why he didn't flash. General Beckman always needed to know things and Chuck was so tired of helping her squeeze out every bit of information that the intersect had. Some days, Chuck just wondered why they didn't just abduct him and lobotomize him, so all he did was flash. No silly nerd to get in the way.

Chuck had heard whispers about a new intersect being constructed in Washington, but he didn't dare ask about it. They would most undoubtedly lie to him anyway. There was something, actually someone who made Chuck's day a little brighter. She was the reason he sometimes enjoyed having the Intersect. Sarah Walker. He didn't know that much about her, but he couldn't help but be enthralled by her. She was beautiful, sweet, smart, and would kick your ass, as soon as look at you. All of these attributes Chuck loved about his handler.

They had their up and down moments in the past, first with Chuck not sure that he could trust her. Followed by the lie that they told themselves, _I'm sorry Chuck, no._ He still remembers her uttering, and it still gave him a bad feeling in his gut. It wasn't more than a week after that they shared their first kiss, when they believed that they were going to die. Quickly followed by the return of the, thought dead, Bryce Larkin. He was Sarah's ex and Chuck's nemesis in much more than just love. After Bryce made them aware of a rogue group inside the CIA, who wished their hands on the Intersect, the relationship between he and Sarah seemed to have stalled, before it had really ever started. She said she wouldn't become involved with him because it would be unprofessional, much to Chuck's dismay.

Sarah Walker had been told it was time to quit the 'Wienerlicious' job, which she had been maintaining as a cover to protect Chuck. This however was the only order she was given, _quit your job._ Those were their exact words. Sarah believed it to be the worst order she had ever been given, as it made no sense. If they were firing her as Chuck's handler, they would have told her. Leaving her to ponder was not a smart thing for anyone to do. Sarah got dangerous the more she thought about her emotions. It wasn't a good idea for anyone to be near her when she was at this very moment.

Sarah had heard through the grapevine, that a new intersect was being constructed. Bryce Larkin was the obvious choice for the successor to the Intersect from the government. Bryce Larkin, talk about conflicting emotions. He had broken her heart when he had stolen the Intersect from the government. Then he reappeared, just when she felt that she was ready to move on. She loved him and hated him. Then there was Chuck. He was simpler, but the situation was still just as complicated. She loved him too, but couldn't expose her emotions because she had to protect him.

A new message appeared on her phone, it was from Casey. _Walker, we need to talk. Meet me at the hideaway. _The hideaway was Casey and Sarah's secret spot that seemed to have a natural jamming signal so that if need be, they wouldn't be monitored. _Why would Casey want to meet there_, Sarah wondered to herself.

The hideaway was under an overpass, between Interstate 5 and Western Ave. Sarah pulled up and waited for Casey to arrive. A 1985 Crown Victoria pulled up behind her, Casey hoped out of it.

"Agent Casey?"

"Agent Walker."

"What are we doing here?"

"It's about Chuck."

"Chuck? What about him?

"I got some orders that I am supposed to follow, and I will."

"What orders, Casey? What's going on?"

"I have been ordered to eliminate the Intersect, when the new intersect comes online."

Sarah took a step back. She reached for the small of her back, putting her hand on her gun. "What?"

"Don't worry; I am here to warn you about what I plan to do."

"You're warning me?"

"Roger."

"I don't get it Casey? You tell me you're going to kill Chuck, but you come here and warn me?"

"I got orders, Walker."

"Then defy them, defy your orders Casey! I have seen you around Chuck. You care about him in your own way."

Casey grunted.

"I knew you did." Sarah recognized it instantly. "We can run, Casey, we can run together."

"No, I can't disobey my orders. Get out of here Walker, go find Chuck."

Sarah was conflicted, she wasn't sure she should turn her back on Casey. He had grown warmer toward her, but he was still a killer. She wanted to protect Chuck from him, even if Casey wasn't with them, she would take him on the run. What about Chuck's sister and his friends? Chuck would never forgive her. Her mind swirled with thoughts, until finally, Sarah made her decision.

A shot went off.


	2. Chapter 2

Disclaimer- I do not own Chuck, or it's characters-sadly

The Runaway Intersect

**Chapter 2**

Casey had his gun out, it was smoking. The humming traffic above them had swallowed the sound of the shot. Sarah Walker was shocked about what she had just witnessed. Blood pooled in a small stain below him. Casey had shot himself.

"Casey," Sarah shouted.

The wound on Casey's shoulder seeped blood. He fell to a knee and held out his gun to his partner. "Take it. Take it and run."

Sarah walked over to Casey and took the gun from him, clicking the safety on.

"Thank you Casey, thank you for this."

Casey grunted, falling to the ground, his consciousness leaving him. "You're my enemy now." This was the last thing his partner heard him utter as she turned and ran.

Sarah headed toward her car. It was only a matter of time before the government knew what had happened here. Whether Casey told them or not, they would find out. She needed to find Chuck.

The BUYMORE was nearly empty; everyone was out enjoying the beautiful day outside instead of spending it shopping for indoor toys. Chuck was tired. The day seemed to drag on and on. He had a "date" with Sarah that night, thinking of that was the only thing keeping him going. He knew that she enjoyed going on the "dates" with him, as well. She seemed to like being treated (acting) like a normal girl. It almost seemed that she was not used to it, which to Chuck just seemed strange.

Chuck suddenly noticed Sarah walking into the BUYMORE, looking around. He waved to her from the Nerd Heard desk that he usually sat at, and where they had first met. She walked quickly toward him, ignoring the slack-jawed employee's that she had become accustomed to.

"Chuck, we need to leave, now!" Sarah said sternly under her breath.

Chuck's face dropped. "What? What's happened Sarah?"

"I will tell you later, let's go."

"But-"

"Let's go!"

Chuck jumped over his desk, his Chucks landing firmly on the ground at the other side. "Okay, let's go," sounding less than enthused.

The car ride outside the BUYMORE parking-lot was not exactly a comfortable one. Sarah wanted to tell Chuck what happened, but couldn't find the words to say. How exactly do you tell a guy that one of his protectors was ordered to kill him and, as far as she knew, was going to? Before he did however, he needed to warn the other protector and then wound himself.

"So where are we going?" Chuck finally asked in a low tone.

"Away. As far away from anyone we can get." Sarah said simply.

"Do you mean that my cover is compromised?"

"No. Not exactly."_ Just say it_, Sarah thought to herself.

The car left the parking-lot and started to speed down the roads of Burbank.

"Then what is going on, Sarah?" It had been a very long time since Chuck had raised his voice to Sarah. It usually involved her relationship with him. She was the one that usually initiated the yelling.

"You have been targeted for execution. Major Casey is supposed to kill you when the new Intersect goes online tonight. I am sorry Chuck, but I have to take you away from here.

"You're committing treason?"

Sarah laughed. She could not believe the sweetness of the man sitting next to her. She had just told him he may die tonight, and he is worried about her.

"Did I say something funny?" Chuck said annoyed.

"No, I think you are too sweet. I tell you this horrible news, that you may die, and all you can do is think about the other people involved."

"Speaking of which. What is going on with Casey, he isn't really going to kill me is he?"

Sarah took the on-ramp toward Interstate 5, accelerating to ten miles above the speed limit.

"I can't tell you Chuck, because I don't know myself. He shot himself so that you and I could run but he also told me that I was now his enemy."

"Casey did what? How could he do such a thing?"

"He's okay, Chuck."

Chuck wouldn't respond to her, his head turned facing his window.

_Emotional shutdown_, she thought. "Chuck we need to get out of LA, lose this car and then changer our appearances, all which in the next 24 hours."

"Or," Chuck said sadly.

"We are as good as captured; they would kill you and fire me for assisting you in your escape. That's the best scenario that I can come up with."

A heavy whirling sound arose from above them, startling them both out of their conversation. A black chopper zoomed passed them, from what seemed like nowhere.

"Whoa," Chuck expressed, looking up out of the windshield.

"Damn it" Sarah dropped her foot hard on the gas. "How did they find us so quick?"

"You sure it's us that their looking for?"

The chopper turned. A man, with what looked like a sniper rifle, became visible at the side door. He looked through his scope and pointed it directly at Chuck.

He fired a shot, and Sarah veered to avoid it. A ping sound came from the passenger mirror.

"Looks like, you want to ask him?" Sarah asked, now in full agent mode. She grabbed Chuck by the collar, yanking him down. His head landed on her lap, chest grazing the stick shift.

Chuck's heart pounded, half from adrenalin, and half from being so close to her.

Another shot was fired from the man in the helicopter. This bullet created a hole in the windshield on the passenger side, ripping the stuffing out of the headrest. They were aiming for Chuck.

Sarah Walker tried something stupid, as she sped down the Golden State Highway. She pulled to the side of the road, spinning her car around to face the other direction. It was a good thing that Chuck couldn't see what was going on, if he did, he would freak out. She pulled back onto the road, going against the traffic this time.

"Sarah, what's...?"

"Don't worry Chuck," Sarah said calmly.

Chuck couldn't help but to worry, they had someone shooting at them, and a now seemingly nuts protector, driving on the wrong side of the road.

Several more shots hit the back of the car, shattering the back windshield, as the helicopter tried to retake the advantage. Sarah turned her car onto an off-ramp, grinding the paint of the car against the wall of the off-ramp to avoid traffic. Sarah turned the car onto the dirt and pulling up behind the off-ramp. She pushed Chuck back to an up position, turning the car off.

The helicopter could still be heard, circling from somewhere above them. Sarah got out of her car, Chuck followed suite, understanding what she wanted. Sarah ran in front of the next passing motorist, driving a 69' Dodge Charger, waving her gun at them. They stopped inches short from hitting her, swearing profanities out of their window. Sarah walked up and pulled them out of the car and onto the side of the road. Sarah got into the car, enjoying the thrill of escape, a bit more than she probably should.

"Sorry," Chuck stammered, getting into the passenger side.

Sarah floored the gas, peeling out. "Well at least we got rid of the car," she said with a smile. They traveled down the quiet side streets of Burbank, the helicopter hummed into silence in the background. They were safe, at least for now.

Inside an undisclosed CIA hideout, Major John Casey had pulled the bullet that he had fired into himself. He was throwing his arm into a sling, when General Beckman appeared on the monitor in front of him, wearing the same old scowl.

"What happened, Major?"

"It was Walker. She must have somehow discovered our plans for Chuck."

"We have already sent a team after her vehicle, unfortunately we lost them."

Casey grunted, trying not to let slip the grin he wished to express.

"I want you back out there tracking them; you are the agent that has spent the most time with both Walker and Bartowski. At least when they were together, we have another agent coming in, he knows them both better than any of us. He may know where they are planning on going, even before they do."

"Let me guess..." Casey said under his breath.

"Bryce Larkin."


	3. Chapter 3

**Chapter 3**

Outside of Salton, CA

At a no-named gas station off the beaten path, Chuck and Sarah were refueling and grabbing any other necessities that they didn't already have. They had been on the road for about three hours, before the fuel light had gone off on their new ride. It was nearly dark, Sarah believed that it was best they turn in early as they government would likely be looking for them to travel at night to avoid pursuit. Sarah was smarter than that, however, as she knew all the tricks in the CIA handbook. They had done only two things on Sarah's list, which she wanted them to do. First, get out of LA and second, find a new car. Although this new car was almost as hot as her original had been.

Any one person that saw them was a potential threat to their safety, the owners of the Charger had most likely reported it stolen and given the police her and Chuck's descriptions. Sarah spotted a security camera nosily watching the single pump. Now the gas station attendant most likely had them on camera, so it wouldn't be too long before someone would be back on their trail. "Chuck stay in the car, I'm going to pay and grab a few more essentials."

Upon entry, Sarah noticed the attendant wasn't paying attention to them his had his eyes glued to the TV, an Oakland A's game was on and the man was making sure he didn't miss a second of it. She grabbed a liter of water and two bottle of hair color, one blonde, one brunette. She would wonder why a gas station would carry such things another time, for now, she counted her blessings. As she went to pay, she made sure that she gathered up all her feminine charms to lull the attendant into a trusting mood. "How's it going," Sarah said in her best flirty voice.

The attendant had turned his attention from the A's baseball game and turned toward Sarah, his jaw visibly dropping. "Been…good," he stammered. "Got fuel too?" He continued, trying to find his composure.

"Course, do you get many thieves out here in the boonies?" Sarah asked, looking past the clerk and to the monitor broadcasting the pump she had just left.

"Nah, the boss wanted them installed just in case, but we don't get nothing but honest forks around here. There only on when he's here to give him peace of mind. Is it going to be cash or charge?"

Sarah handed him a hundred dollar bill, "Keep the change, and don't work too hard." She hoped that her flirting and extra pocket change would help the man forget that he ever saw them.

She got back into the Charger and handed the bag to Chuck. "We need to find a motel in about an hour or so, keep your eyes peeled."

"Sure thing," Chuck said with a heavy breath.

They found a semi-secluded motel, another 50 miles down from where they left the clerk. It was about as strategically pleasing as they were going to find on such short notice. With a forest to the east and the Salton Sea to their west, they only had two directions that their pursuers were most likely to come from. They hid the vehicle best they could, toward the back, by the tree line. Sarah made her way to the office, having Chuck stay outside to be the lookout, yelling if he spotting anything resembling danger.

"Will do. I'll make sure to let out my most girlish shriek, so you know when to come running."

Sarah gave him a smile, "Good boy." _He was finally coming back to his senses_.

"I'm going to ignore that dog reference."

Inside she found a creepy receptionist. Like the attendant he was fixed to the boob tube, only he was watching something far less family friendly. Beside him were the room costs. A single room was $40 and a double was $60. She rang the bell to get his attention. He pulled it out of her reach, once it had gone off. He turned ever so slightly toward her. "Need a room?" his eyes still tightly secured to the TV.

"If it wouldn't be too much trouble?" She said, once again in her best flirty voice.

His eyes met hers, "You all alone, sweetie?"

She gave the bubbly response of "Uh, yeah." She thought that she almost got a free room, until the man noticed Chuck outside the door.

"That your boyfriend?" His eyes watching Chuck.

"Ew…no, that's my brother. Can I have a double?"

"I'm book on my doubles, but I can give you a deal on a single, since you're a sweet thing. How does twenty bucks sound?"

"Great, thank you so much."

He handed her a key, "It's the just on the other side of the office, we will be sharing a wall."

Sarah mustered as much excitement as she could, which only came in the form of a smile as she headed for the exit.

Chuck was amazed what an attractive blonde could do with just her looks. Although once they entered the motel room, he thought differently. The smell alone was almost enough to make Chuck run for the hills. The place was a sty. Sarah however entered without a word; after all, it was shelter.

"They only had a single. So Chuck, take the bed, I will need to stay up and watch for visitors in the night."

"And then you will be tired all day, not much of a plan now is it." Chuck replied.

Sarah sighed, and opened her mouth to rebut. Closing almost as quickly, _he had a valid point_, She thought to herself. There was no way she was going to stay focused on protecting him with no sleep.

Chuck eyed the bed and gave a shudder. He didn't want to think about what happened in it since it had been washed, if it had ever been.

Sarah pulled the cover off the bed. She seemed to be thinking the same thing Chuck had been. "Looks like you and are going to be sleeping in here tonight." Sarah said, eying the bed.

Chuck turned a bit pink, at the comment. He knew what Sarah meant, but he still couldn't shake the idea of Sarah and himself sleeping in the same bed. "I...I think I'll sleep out in the car."

"Chuck, don't be ridiculous, this is perfectly safe. Besides I can't protect you in the car." Sarah replied in a soft spoken voice.

"I guess," Chuck said nervously.

"We need to decide whether or not we want to head into Mexico yet, or just say in the US. They are must likely going to be checking for us at the border, so we will most likely have to hoof it. This, of course, means that we could potentially be shot at again."

"Decisions, decisions. I'll do whatever you think is best. This really isn't my forte, as you already know. I don't really feel like getting shot again though."

"I am going to take a shower, you stay put. We don't have to make a decision until the morning."

"You can't protect me from there either, you know." Chuck joked.

Sarah rolled her eyes and entered the bathroom, carrying a box of supplies in her hand.

Washington D.C.

It was finally time, the new intersect was ready to be uploaded. General Beckman still looked a bit annoyed, the old intersect had still not been captured. She had a long list of candidates she wished to pick for the new intersect. The top of the list being Agent Larkin, he would have to wait, however. He was of use elsewhere at the moment. But she needed some she trusted with the task of destroying the old intersect before it fell into enemy hands. She wouldn't let that nerd use its abilities against her.

The second agent on her list was a man by the name of Daniel Shaw. He was a good agent with a sad past. She had ordered another agent to assassinate his wife, assuming she was part of the group known only as The Ring. It was a mistake, one that she would admit to, that is to anyone who wasn't Shaw. He had no knowledge of this indiscretion, and it made him a stronger agent because of it. In the back of her mind however, she hoped he would never know the truth, knowing that it would turn one of her best agents into a rouge operative, as many have been doing in the last few hours.

Daniel Shaw was one of the good guys. He had caused enough to others since his start with the CIA. He would make it his mission to takeout everyone who was involved with his late wife's death. After the phone call with Beckman, he knew that he could finally make some headway with this new tech, called the Intersect. But to anyone else he would say that is was time to give back to his government, which had given him so much already.

He was placed into the intersect room, a small room with several white panels, that covered all sides. The only thing of note inside the room was a computer, which looked like it had been around since the early 80's. He stood before it and waited for it to connect.

The machine before him hummed to life, a download bar began to run on the screen. Images began to flicker around him, as the download bar reached 100%. A flood of images and data surrounded him on the once white panels. Those same images enveloped agent Shaw's mind, making him dizzy, and his legs rubber. He maintained his composure as the sequence of images ended. He was ready, he was the Intersect.

Just outside of Bombay Beach

When Sarah Walker emerged from the bathroom, after what seemed like forever. Chuck had to give her a second glance, her hair was now short and brown instead of long and blonde.

"Sarah, what did you do?"

"I cut my hair, and then dyed it, obviously."

"But..."

"Chuck, we need to change our appearance, and this is me changing mine. I have one for you as well," she pulled out a box with a blonde woman on the box.

"I don't want to look like Awesome."

Sarah chuckled, "Don't worry Chuck, I promise you will not look like him. You don't have his muscles."

"Ouch, Thanks. Can we wait until morning to do that?"

"I suppose. Barring any unwelcomed company."

Chuck climbed into bed and realized that he didn't know what to do with his hands, he finally decided to place them under his rump, they would be numb, but at least he could trust them that way. Sarah had climbed into bed with him, unwise to the dirty thoughts that traveled through his head. They were alone together, they were on the run, _and what could it hurt. She's protecting me, what if something happens and she is too emotionally involved with me to deal with it. She may want to, and I know I do, so what would be the harm. _Chuck edged a bit closer to Sarah.

"Goodnight, Chuck."

"Sorry, just getting situated," he lied.

"We do need to get an early start on tomorrow, just in case Casey or some other government stooge is still on our trail."

"Goodnight then." Chuck turned off his light on his side of the bed.

Sarah Walker's heart sank. She was able to finally be with the man that she had fallen for, and she pushed him away, because of her spy training. She didn't really believe that anyone was close enough to be trailing them this closely. Maybe Casey, if he hadn't shot himself.

Sarah closed her eyes and dreamed of a wonderful day, a day where she and Chuck could be free to live together, free to love each other. It, unfortunately, was only a dream.


	4. Chapter 4

**Chapter 4**

Burbank, CA

A well-dressed man arrived outside the BUYMORE; he entered the access code that let him into the store, thanks to Casey. It seemed far less chaotic that the last time he had been there. There were no frenzied shoppers looking for the best deals and no gunman looking for the Intersect, with the exception of himself and Major Casey. Bryce Larkin was more than happy to walk into a place that wasn't already, or soon to be, a war zone.

Inside the home theater room, Casey, with a new sling across his left arm, took what remained of the guns and ammunition he had kept in the console for an Intersect emergency. Although this wasn't the emergency he had wanted, he was more than willing to follow through with it. Or so he told himself. Being partnered with Bryce Larkin was something that Casey had never planned on. If he had it his way that agent would have 6 feet in the ground almost a year ago. Traitor or not he destroyed a multi-billion dollar facility, and to be blunt, he didn't like his smug little face.

"Casey." Bryce said coldly, as he entered the room.

"Larkin." The Major echoed his tone.

"It feels like just yesterday that you killed me."

Casey closed up his secret weapon cash and circled around to stand near Bryce. "We aren't going to start talking about are feelings are we? I've had enough of that these last few months dealing with your buddy Chuck."

"Believe me. I want to get this done as quickly as you do. So we can get back to being real spies."

"Need a piece?" Casey handed him one of his NSA issued Browning HI-Power's he had been keeping in the console.

Bryce looked at the gun, "Got anything with a little more kick?"

"The gun that killed you once isn't good enough for you?"

Larkin flashed his Glock that was sticking out of the back of his pants. "I'm still here, aren't I?"

Casey grunted, as Chuck would have described as his number seven grunt. "Well, come on, I will tell you what we have so far, on the way.

"On the way to where?" Bryce asked as they both exited the Home Theater room.

After locking the store back up, they headed toward Team Bartowski's old mission van, which was parked in the back of the BUYMORE parking lot. Casey threw the keys to Larkin, and noticed two familiar Nerd Herders that he was definitely not going to be missing, Jeff and Lester. If he ever saw a more dangerous combination of smart, lazy and crazy, he would eat his shirt. They were being booted out of Bennigan's again, probably for getting drunk again and being a bit too friendly with their waitress. He hoped that he wouldn't ever have to deal with their shenanigans again. He entered the back of the van as they were being pushed to the curb.

Bryce took the wheel, and for what seemed like forever, there was a strained silence between the two men. Neither man was sure that they could trust the other.

"Where we headed?" Bryce finally broke the silence.

"It sounded like they were headed southwest, probably toward the Mexican border. Though, I doubt Walker would chance crossing at the checkpoint. She's good, I'll give her that, but even she couldn't foresee all the possible outcomes. Besides, she wouldn't endanger Chuck, if she could help it. By the way, I'd go down I-5 if it were up to me."

"Interstate 5 works for me." Bryce switches the subject. "I get that they bonded, but I never expected Sarah would do something like this, going rogue. What's going on between them?" Bryce tried to mask his jealousy behind a professional tone, but it was clear to Casey what he was getting at.

"Agent Walker doesn't think we should kill a civilian, rather adamantly, judging by the bullet hole she put into my shoulder. Or maybe she was thinking about you, he is your supposed friend after all. Maybe she didn't want to see you in any more pain."

"That's part of the job, Sarah knows that, or at least she should. She's been there before, with me." Bryce turned onto to Interstate 5.

"Lady feelings," Casey said under his breath, covering it up with a loud quizzical grunt. "Let's just head toward San Diego for now. Walker had some friends down there last I knew, we could pay them a visit, and see if we get lucky. Otherwise, we can see what the Agency has for us in a couple of hours. Now, if you don't mind I think I will get a little shut eye."

"You can possibly-" But when Bryce checked the rear-view, John Casey was already snoring.

Over the New Mexico desert

On a plane bound for San Diego, Agent Daniel Shaw looked over documents containing the past missions with the so called 'Team' Bartowski. Agents Walker and Casey booth seemed impressive enough, and the Intersect gave him a good bit of info involving their exploits before and during their partnership with the rogue man named Charles Bartowski, A.K.A. Chuck. There is very few people that could accomplish everything they did in such time frame. It wasn't clear to Shaw, who was responsible most for their success. By the way Agent Casey described Chuck, he was accident prone, defiant and a bit of a loud mouth, not someone you wanted walking around with government secrets in his brain. He understood now why he was tasked with taking him out. Although, he didn't see why all of these resources were being tasked to kill a simple geek, it must be his former handler.

Agent Walker intrigued him the most, she was young and beautiful, and had quite a successful career in the last decade that she had been with the agency. Although he could find nothing in the files or his minds own database about what she did, or who she was before she became an Agent. That shot up red flags for him, she could have been a sleeper agent for someone else, and it's easy enough for some people to pull off an American accent these days.

Major John Casey was nearly as much an Enigma as Walker was; he had a very decorated and patriotic past, and something that Shaw would call a Reagan complex. There was no sign of his existence before Reagan took office back in 1981. He would be the one he would try to find if he thought that he needed any help with Walker or Bartowski.

Agent Shaw's mind surged when he saw a photo of a woman that he almost recognized. At first the surge showed him the word 'Isis' with a confidential file, secondly he saw her picture, with the code name Frost. He took no time in holding up Frost's picture next to Bartowski's, it was clear that there was a family resemblance. _She may prove useful in the coming days_, Shaw thought to himself. That is, if he could find her.

The next picture wasn't hard to place; _he must be Chuck's father_. His suspicions were quickly realized when he surged on the picture, Stephen J. Bartowski, a frumpy looking man. He was described in the file as an eccentric genius and one of the men responsible for the development of the intersect computer system. "Things just got a bit more interesting." Shaw said to himself. "I wonder if he knows his dad made the computer." _Not that it matters. _

Suddenly, another feeling hit him, one that he couldn't quite place. The sensation was new, yet familiar. Something about it told him the Intersect was near. It had to be the Intersect, he was sure of it. However his Intersect didn't surge, it merely vibrated. He thought, just for a moment, that he could sense another presence inside of his mind. He checked out the window and saw only darkness below. He was close to him, he could feel it.

A/N- Thanks for reading, don't forget to review. More Chapters to come.


	5. Chapter 5

**Chapter 5**

Unknown, CA?

Chuck was tired of running. Running to or from what, he didn't know. There was nothing but darkness around him. He heard a scream from all sides of the darkness, a familiar scream. "Sarah?!" his cry echoed. He finally came to a river of blood. He wanted to find Sarah, this was too much blood. "Sarah!" Chuck listened when the scream came again to see where it was coming from; he couldn't pinpoint it.

"Chuck," Sarah's ghostly voice came from the void. "I need to protect you, where did you go. I told you to say in the car." The voice turned wrathful. "Where are you, Chuck, why weren't you there to protect me, we were supposed to be a team." Sarah's voice grew ever more ominous.

"I'm here. I'm right here." Chuck's voice began to tremble. He was going to lose her, and he didn't even know how or why.

From out of nowhere, an athletic man, with black hair an expensive suit, appeared in front of him. "I found you, Chuck." The man raised a gun, which seemed to materialize from nothingness, to Chuck's forehead. With a smile, the man said

"Bang!"

Chuck awoke with a jump.

Sarah Walker sprang into action, like she hadn't even been asleep. "Chuck, what's wrong." She couldn't even count the number of sweat beads across his forehead.

"I…Nightmare…Sarah," Chuck gasped for breath. It felt like the Intersect was overheating, and it was boiling his brain. "Halp…"

Her CIA training was failing her, all she could think of was Chuck dying in front of her and not being able to stop it. His charm, his wit, and his love would be gone forever. An idea popped into her head. She pressed her lips against his.

Chuck's brain didn't feel like it was about to pop anymore, it seemed content enough with what was happening. Kissing Sarah soothed his nerves and slowed his heart. He held his breath and his breathing began to slow. "What…was that?"

"I…I kissed you…" Sarah muttered. "…and you held your breath."

"Wow," Chuck scooted toward Sarah's side of the small bed. "Can we do that again? Without the hyperventilating I mean."

Sarah beamed. "As long as you're OK."

"Shut up and come here." Chuck, filled with renewed life, touched her chin and leaned toward her, his lips pursed. Their mouths collided in blissful tenderness. This kiss was far more potent that the first kiss she planted on him tonight, nearly as potent as their first, when they thought they were going to die. He took her waist with his free hand. She positioned her hands around his neck, and through his curly mop of hair. The two former Co-workers forgot about the world, and savored what they had been missing. They could have stayed in this place forever, just the two of them.

The play changed when Sarah eased Chuck's hand toward second. He looked at her, as if to ask, _you sure?_ She responded by kissing his neck, tenderly. It didn't take him anytime to remove her shirt and his. He fumbled for his wallet on the nightstand. After a moment of struggling, he discovered what he was looking for.

The moment they entered into carnal delight would stay with them for the rest of their lives. Their eyes held, never blinking, never wavering, held for as long as they were together. Their bodies did not want to separate, ever again. The sun came and so did they.

The bed that they had been disgusted with became a place they didn't want to leave. But, it was time to go. If they didn't get moving, they wouldn't be able to share each other for much longer. "Chuck, you still need to dye your hair, it should help you not to stand out." Sarah grabbed the box of hair color and held it up to him.

"Okay," Chuck agreed, begrudgingly. "But if I come out looking like Captain Awesome, you better not laugh. Or you're going to get it."

"I'm sooo scared."

Chuck grabbed his pillow and playfully threw it at her. Before she could return the favor, he hurried into the bathroom and shut the door.

"Coward." Sarah laughed, throwing the pillow at the door.

While Chuck was in the shower, Sarah thought it might be good to see if any of her old friends could give them support, or a potential safe haven. There was an old payphone just outside of the motel office that she spotted when they arrived and hoped it still worked. She threw on her clothes that were now spread across the room and headed for the door. Sarah moved right for it, fiddling with the three quarters that she had picked out of Chuck's pants pocket. _I'll owe him._ She picked up the receiver, threw in seventy-five cents, and began to dial a number. "Carina. It's Sarah. I don't have time to talk, are you still in San Diego? Good. Listen, I am in a bit of a situation, do you have any trusted contacts in Mexico? No. How about anywhere in the southwestern states? Yea, what's the number? Got it, and Carina, if anyone asks you about me, tell them that you haven't talked to me okay? Sorry, got to go, Thanks."

Chuck couldn't stop grinning. He had nearly forgotten about his horrible nightmare and the fact that he was a marked man, though those thoughts were slowly creeping their way back into the front of his mind. Being with Sarah made it feel manageable. He only wished he could have said goodbye to Morgan and Ellie. _Elli, she was all alone now. First Mom left, then Dad, and now me._ Chuck looked at his new hair in the mirror. _At least she has Devon, he is a good guy, in spite his nickname. Morgan will still be hanging around her too, with Anna._ He chuckled to himself. _That would be a sight to see, just like the new hairdo._

When Chuck exited the bathroom, Sarah had her bag on her shoulder, ready to go. She took one look at Chuck and smiled, covering her mouth, looking ready to laugh.

"I asked you not to laugh."

"I'm not laughing. You don't look like Awesome, really you don't. Your hair is almost pure white." Sarah tried to hold in her laughter, unsuccessfully. "I guess you will be noticed, I need to find you a hat."

"Get over here," Chuck took Sarah's waist and brought her in for a kiss. "I told you that you were going to get it."

"Smooth." Sarah smiled, but her tone quickly changed. "Now get dressed, we have to get going. Oh and by the way, what was that nightmare you had last night."

"Typical nightmarish stuff you'd expect with everything that happened yesterday. I couldn't find you, then I saw blood, and then your voice got all scary. The weird part was the end, and by weird I mean terrifying. A man I didn't recognize showed up and pulled a gun on me, saying that he found me." Chuck spoke quickly.

"He shot you?"

"No, just said 'BANG' that's when I woke up." Chuck struggled to put on his pants. "The funny thing was I think the Intersect has something to do with that man, and the dream."

"I would as how you knew, but I guess if think that's what it was I believe you. You think that man was the new Intersect? You think he can track you?"

"Don't know," Chuck said with a shrug, after tying his Chucks. "At least I remember what he looks like, if I spot him in the real world, I'll give you a shout."

"At least there's that, let me know if you see him in your dreams as well."

"K, but I doubt he will be showing up again."

Sarah shot him a puzzled look, "Why's that?"

"Cause, I will be dreaming about last night, for many nights to come."

She rolled her eyes. "Get out of here." And kissed him.


End file.
